The comparative phylogeography of marine species with contrasting dispersal potential across the southern Caribbean Sea was evaluated by the presence of two putative barriers: the Magdale-na River plume (MRP) and the combination of the absence of a rocky bottom and permanent upwelling in the La Guajira Peninsula (ARB+PUG). Three species of rocky shallow bottoms were selected with different dispersal potentials: Acanthemblemaria rivasi (PLD < 22 days), Cittarium pica (PLD < 6 days), and Nerita tessellata (PLD > 60 days). We generated a set of SNPs for the three species using the ddRad-seq technique. Samples of each species were collected in five locations from Capurganá to La Guajira. For the first time, evidence of a phylogeographic break caused by MRP is provided, mainly for A. rivasi (AMOVA: ФCT = 0.420). The ARB+PUG barrier causes an-other break for A. rivasi (ФCT = 0.406) and C. pica (ФCT = 0.224). Three populations (K = 3) were identified for A. rivasi and C. pica, while N. tessellata presented one population (K = 1). The Mantel correlogram indicated that A. rivasi and C. pica fit the hierarchical population model, and only the A. rivasi and C. pica comparisons showed phylogeographic congruence. Our results demon-strate how the biological traits of these three species and the biogeographic barriers have influ-enced their phylogeographic structure.